Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this
to extract flanking regions for cloning. If the result of the multiple sequence alignment is
not as expected, these results could be used for further investigation.
qseqid
sseqid
percentage.identical
alignment.length
no.mismatch
no.gap.openings
qstart
qend
sstart
send
evalue
bitscore
0
TraesCS5A01G083700
chr5A
100.000
2816
0
0
1
2816
109345572
109342757
0.000000e+00
5201.0
1
TraesCS5A01G083700
chr5A
91.977
511
31
3
3
513
368150882
368151382
0.000000e+00
708.0
2
TraesCS5A01G083700
chr5D
93.534
1160
60
7
651
1807
105350788
105349641
0.000000e+00
1712.0
3
TraesCS5A01G083700
chr5D
96.318
679
24
1
2138
2816
105349287
105348610
0.000000e+00
1114.0
4
TraesCS5A01G083700
chr5D
89.691
291
21
5
1839
2121
105349561
105349272
2.060000e-96
363.0
5
TraesCS5A01G083700
chr5D
97.368
38
1
0
1800
1837
105349635
105349598
6.510000e-07
65.8
6
TraesCS5A01G083700
chr5B
94.004
984
31
11
1839
2816
115319013
115318052
0.000000e+00
1465.0
7
TraesCS5A01G083700
chr5B
90.278
864
54
14
649
1492
115320298
115319445
0.000000e+00
1103.0
8
TraesCS5A01G083700
chr5B
91.409
582
36
6
1270
1837
115319631
115319050
0.000000e+00
785.0
9
TraesCS5A01G083700
chr5B
84.021
194
24
3
1234
1420
115319620
115319427
2.230000e-41
180.0
10
TraesCS5A01G083700
chr7A
91.346
624
37
10
3
614
325896877
325896259
0.000000e+00
837.0
11
TraesCS5A01G083700
chr2A
91.228
570
38
7
3
570
716407235
716406676
0.000000e+00
765.0
12
TraesCS5A01G083700
chr2A
91.281
562
39
4
1
553
726863327
726863887
0.000000e+00
758.0
13
TraesCS5A01G083700
chr2A
88.073
545
55
6
10
554
163683343
163682809
3.060000e-179
638.0
14
TraesCS5A01G083700
chr2A
94.444
144
8
0
1
144
209062052
209062195
3.650000e-54
222.0
15
TraesCS5A01G083700
chr2A
94.776
134
7
0
1
134
616641618
616641485
2.840000e-50
209.0
16
TraesCS5A01G083700
chr2A
95.798
119
5
0
1
119
449233296
449233178
2.860000e-45
193.0
17
TraesCS5A01G083700
chr1A
89.855
552
45
8
71
614
491499051
491498503
0.000000e+00
699.0
18
TraesCS5A01G083700
chr4A
93.763
465
22
4
156
614
462074848
462074385
0.000000e+00
691.0
19
TraesCS5A01G083700
chr3A
87.458
598
63
9
1
593
549929298
549928708
0.000000e+00
678.0
20
TraesCS5A01G083700
chrUn
87.978
549
54
9
74
613
290876063
290876608
3.060000e-179
638.0
These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the
BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are
purely upstream or downstream may be removed if they don't overlap both primers.
query
scaffold
start
end
length
rev.comp
avg.bitscore
max.bitscore
avg.percent.identical
query.start
query.end
num_hsp
groupid
homo_length
0
TraesCS5A01G083700
chr5A
109342757
109345572
2815
True
5201.00
5201
100.00000
1
2816
1
chr5A.!!$R1
2815
1
TraesCS5A01G083700
chr5A
368150882
368151382
500
False
708.00
708
91.97700
3
513
1
chr5A.!!$F1
510
2
TraesCS5A01G083700
chr5D
105348610
105350788
2178
True
813.70
1712
94.22775
651
2816
4
chr5D.!!$R1
2165
3
TraesCS5A01G083700
chr5B
115318052
115320298
2246
True
883.25
1465
89.92800
649
2816
4
chr5B.!!$R1
2167
4
TraesCS5A01G083700
chr7A
325896259
325896877
618
True
837.00
837
91.34600
3
614
1
chr7A.!!$R1
611
5
TraesCS5A01G083700
chr2A
716406676
716407235
559
True
765.00
765
91.22800
3
570
1
chr2A.!!$R4
567
6
TraesCS5A01G083700
chr2A
726863327
726863887
560
False
758.00
758
91.28100
1
553
1
chr2A.!!$F2
552
7
TraesCS5A01G083700
chr2A
163682809
163683343
534
True
638.00
638
88.07300
10
554
1
chr2A.!!$R1
544
8
TraesCS5A01G083700
chr1A
491498503
491499051
548
True
699.00
699
89.85500
71
614
1
chr1A.!!$R1
543
9
TraesCS5A01G083700
chr3A
549928708
549929298
590
True
678.00
678
87.45800
1
593
1
chr3A.!!$R1
592
10
TraesCS5A01G083700
chrUn
290876063
290876608
545
False
638.00
638
87.97800
74
613
1
chrUn.!!$F1
539
AutoCloner calculated primer pairs
These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3),
whilst remaining within the specified product range where possible.
Listed here are all possible primers based on the multiple sequence alignment and SNPs generated
previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work
during PCR or sequencing,
these could be used as alternatives.